According to the Chattanooga FC Website, New York Cosmos B did indeed have the better record, and therefore right of refusal for home-field advantage, but they agreed to play the match in Chattanooga.
Immediately following Saturday’s matches, work began to determine the
best location for the 2015 Championship game. While their #1 seed
gives the NY Cosmos B the right of refusal for home-field advantage,
Chattanooga was able to secure the home field advantage, with the
Championship to be played at Finley Stadium’s Davenport Field on
Saturday, August 8 at 7:30pm.
They also give a couple of reasons why NY Cosmos agreed to this, which could be summarized as "bums on seats".
While there were a number of factors at play, according to CFC board
member Tim Kelly, one of the most persuading arguments to bring the
game to Chattanooga was the combination of a world-class soccer
facility and the strongest fan base in the NPSL.
“In a league where most teams enjoy the regular support of a few
hundred fans, our fan-base here Chattanooga is envied—and our
partnership with Finley stadium insures a great experience for fans
and players alike. Teams want to play here.”
Reading between the lines, especially the words "work began" in the first quote, I think that means that the teams negotiated that a share of that gate money (18,227 fans attended, a national record for an amateur match) went also to NY Cosmos B, and this share was more than they would have got by holding the match at home.